function varargout = importSCaseDev(varargin)
% IMPORTSCASEDEV MATLAB code for importSCaseDev.fig
%      IMPORTSCASEDEV, by itself, creates a new IMPORTSCASEDEV or raises the existing
%      singleton*.
%
%      H = IMPORTSCASEDEV returns the handle to a new IMPORTSCASEDEV or the handle to
%      the existing singleton*.
%
%      IMPORTSCASEDEV('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in IMPORTSCASEDEV.M with the given input arguments.
%
%      IMPORTSCASEDEV('Property','Value',...) creates a new IMPORTSCASEDEV or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before importSCaseDev_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to importSCaseDev_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help importSCaseDev

% Last Modified by GUIDE v2.5 15-Jan-2019 16:51:28

%% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
    'gui_Singleton',  gui_Singleton, ...
    'gui_OpeningFcn', @importSCaseDev_OpeningFcn, ...
    'gui_OutputFcn',  @importSCaseDev_OutputFcn, ...
    'gui_LayoutFcn',  [] , ...
    'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function importSCaseDev_OpeningFcn(hObject, eventdata, handles, varargin)
%% --- Executes just before importSCaseDev is made visible.
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to importSCaseDev (see VARARGIN)
%--------------------------------------------------------------------------
% Choose default command line output for importSCaseDev
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes importSCaseDev wait for user response (see UIRESUME)
% uiwait(handles.figure1);
movegui('center')

%--------------------------------------------------------------------------
%% Customized by JSM 2018/10/26
% Setting default values for some global variables

% Default directory = the current directory
handles.script_dir = pwd;
cd([pwd '/../../../../']);
handles.home_path = pwd;
cd([pwd '/data/']);
handles.base_dir = pwd;
cd(handles.script_dir);

% Radiobuttons
% *handles.acquisition_stage* => might be 'Normal' or 'Pathologic'
set(handles.radiobutton_Pathologic,'Value',1);
handles.patient_group="P";
% *handles.shoulder_side* => might be 'Right' or 'Left'
set(handles.radiobutton_right,'Value',1);
% *handles.acquisition_stage* => might be 'Preop' or 'Postop'
set(handles.radiobutton_preop,'Value',1);
% *handles.output_dir* => importation folder. By default the current dir.
set(handles.output_dir,'String',pwd);
% *handles.body* => might be 'Shoulder', 'Elbow' or 'Other[]'
set(handles.radiobutton_shoulder,'Value',1);
% *handles.CTlabel_text* => might be '-1', '-2', ..., '-1p', '-2p', ...
set(handles.CTlabel_text,'String','-xxx');

guidata(hObject,handles); 

function varargout = importSCaseDev_OutputFcn(hObject, eventdata, handles)
%% --- Outputs from this function are returned to the command line.
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;

%% ======================================================================
%% "Create Functions" execute during object creation, after setting all properties.

function patient_num_CreateFcn(hObject, eventdata, handles)
%% --- Executes during object creation, after setting all properties.
% hObject    handle to patient_num (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



%% --- Executes during object creation, after setting all properties.
function slider_2Dslice_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_2Dslice (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end
guidata(hObject,handles); 


function edit_otherBody_CreateFcn(hObject, eventdata, handles)
%% --- Executes during object creation, after setting all properties.
% hObject    handle to edit_otherBody (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end
guidata(hObject,handles); 


function edit_extra_CreateFcn(hObject, eventdata, handles)
%% --- Executes during object creation, after setting all properties.
% hObject    handle to edit_extra (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end
set(hObject,'String','Write here every extra info...');
% update_infoFields(handles);
guidata(hObject,handles); 



%% ======================================================================
%% "Callback Functions" execute on hObject's action events 

%% ************** Patient Type (group) **************
function radiobutton_Pathologic_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_Pathologic.
% hObject    handle to radiobutton_Pathologic (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_Pathologic
handles.patient_group="P";
set(handles.act3Dview,'value',1)
act3Dview_Callback(handles.act3Dview,eventdata,handles)
patient_num = get(handles.patient_num,'String');
set(handles.patient_num,'String',['P' patient_num(2:end)]);


function radiobutton_Normal_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_Normal.
% hObject    handle to radiobutton_Normal (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_Normal
handles.patient_group="N";
set(handles.act3Dview,'value',0)
act3Dview_Callback(handles.act3Dview,eventdata,handles)
patient_num = get(handles.patient_num,'String');
set(handles.patient_num,'String',['N' patient_num(2:end)]);

%% ************** Start new Patient / sCase **************
function newPatient_Callback(hObject, eventdata, handles)
%% --- Executes on button press in newPatient.
% hObject    handle to newPatient (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% This button lunch the initial check of a folder containing a group of
% sets of CTs. It counts the files per subfolder to clasify them

% Select a limit of minimun dicom files to discard scout scans & other
% small scans as elbows
scoutScanLimit = 30; 
smallScanLimit = 90;

% Choose the main folder for the desired case
newPath = uigetdir(handles.base_dir);
% handles.patient_dir = newPath;
current_dir = pwd;
cd([newPath '/..']);
handles.patient_dir = pwd;
cd(current_dir);

% Check the given path and extract data from every folder and file inside
dirList = dir(newPath);
% Select only the folders from the current path --> folderList
folderN = 0;
for k=3:length(dirList)
    folderN = folderN + dirList(k).isdir
    if folderN * dirList(k).isdir >0
        folderList(folderN) = dirList(k);
        folderN,folderList(folderN).name
    end
end


% Check how many dicom files are in each folder (to discard ScoutScans)
wb = waitbar(0,'Checking folders size');
for k=1:folderN
    % <files> will contain a struct with data of files in the desired
    % folder
    waitbar(k/folderN,wb,sprintf('%s%s%s%i%s%i',"Checking directory ",...
        string(folderList(k).name),": ",k,"/",folderN));
    files=dir([folderList(k).folder '/' folderList(k).name]);
    filesDicom = 0; % Initialitation of dicom files counter
    for n=1:length(files)
        % if is a file and this file is a dicom file, note it
        % (files.isdicom) and count it
        if isfile([files(n).folder '/' files(n).name]) & ...
                isdicom([files(n).folder '/' files(n).name])
            files(n).isdicom = 1; % noting down that it is a dicom file
            filesDicom = filesDicom +1; % counting the dicom files
            % Next line builds a list of dicom file names in cell mode
            folderList(k).dicomList(filesDicom) = cellstr(files(n).name);
        else
            % Otherwise, is not a dicom file and we note it like that
            files(n).isdicom = 0;
        end
    end
    % Each folder has it own counter of dicom files
    folderList(k).dicomN = filesDicom;
    % We add a prefix with the number of files per CT, helping to priorize
    % the importation order
    if ~contains(folderList(k).name,['s' char(string(folderList(k).dicomN))])
        movefile([folderList(k).folder '/' folderList(k).name],...
            [folderList(k).folder '/' 's'...
            char(string(folderList(k).dicomN)) '-' folderList(k).name]); 
        folderList(k).name = ['s' char(string(folderList(k).dicomN))...
            '-' folderList(k).name];
    end
    %% From here it could be commented and eliminated (JSM 25102018)
    % When a folder has few dicom files we can consider that it was a scan
    % scout instead of an interesting CT
    if folderList(k).dicomN < scoutScanLimit
        folderList(k).scanMode = 'scoutScan';
        % Changing the folder name to mark it as scoutScan (if not marked
        % before)
        if ~contains(folderList(k).name,'scout')
            movefile([folderList(k).folder '/' folderList(k).name],...
                [folderList(k).folder '/' folderList(k).name '_scoutScan']); 
        end
    elseif folderList(k).dicomN < smallScanLimit
        folderList(k).scanMode = 'smallScan';
        % Changing the folder name to mark it as scoutScan (if not marked
        % before)
        if ~contains(folderList(k).name,'small')
            movefile([folderList(k).folder '/' folderList(k).name],...
                [folderList(k).folder '/' folderList(k).name '_smallScan']); 
        end
    else
        folderList(k).scanMode = 'CT';
    end
    % Until here 
end

% Makes handles variable visible to other functions in this script
% hanldes.dicomdir = newPath;
guidata(hObject,handles); 


%% ************** Load next CT set **************
function Load_Next_CT_Callback(hObject, eventdata, handles)
%% --- Executes on button press in Load_Next_CT.
% hObject    handle to Load_Next_CT (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Before loading a new set of CTs we should remove the last one
clear handles.data 

% Output Directory update
% if isfield(handles,'patient_dir')
%     handles.base_dir = handles.patient_dir;
% else
%     handles.base_dir = handles.home_path;
% end

% Also remove the fields 'myinfo' and 'mydicom' (they could be just
% cleared?)
if isfield(handles, 'myinfo');
    handles = rmfield(handles, 'myinfo'); % Removing 'myinfo' field from structure in handles
else if isfield(handles, 'mydicom');
    handles = rmfield(handles, 'mydicom');% Removing 'mydicom' field from structure in handles
    end
end

if isfield(handles,'dicomSet')
    handles = rmfield(handles,'dicomSet');
end
if isfield(handles,'dicomSetSorted')
    handles = rmfield(handles,'dicomSetSorted');
end

%% Loading CT files
% Using last directory
if isfield(handles,'patient_dir')
    [handles.dicomlist, handles.dicomdir] = uigetfile('*.*',...
        'Select the images to load',handles.patient_dir,'MultiSelect', 'on');
elseif isfield(handles,'base_dir')
    [handles.dicomlist, handles.dicomdir] = uigetfile('*.*',...
        'Select the images to load',handles.base_dir,'MultiSelect', 'on');
else
    [handles.dicomlist, handles.dicomdir] = uigetfile('*.*',...
        'Select the images to load',home_path,'MultiSelect', 'on');
end

% Showing the dicom name in the interface 
set(handles.text_dicom_name,'String',strcat(string(handles.dicomdir), string(handles.dicomlist(1))));

% Number of dicom files
handles.N = length(handles.dicomlist);

% Set parametres for 2D visualization
set(handles.slider_2Dslice, 'Max', handles.N);
set(handles.slider_2Dslice, 'Value', int32(handles.N/2));
set(handles.slider_2Dslice, 'SliderStep',[1/handles.N 10/handles.N]);
set(handles.slider_2Dslice, 'Min', 1);

set(handles.info_text, 'ForegroundColor', 'black', 'FontWeight', 'normal');

% Read dicom data
try
    % This loop reads all the dicom files and builds a new struct with the
    % information from each row and the data (the images)
    wb = waitbar(0,'Loading DICOM files'); %This  creates a waitbar or progressbar
    L = length(handles.dicomlist); % number of dicom files to load
    for n=1:L
        waitbar(n/L,wb,sprintf('%s%i%s%i',"Loading DICOM metadata ",n,"/",L));
        % Reads the info from each dicomfile
        handles.dicomSet(n) = dicominfo(sprintf('%s%s',...
            handles.dicomdir, char(handles.dicomlist(n))),'UseDictionaryVR',true); 
    end
    for n=1:L
        waitbar(n/L,wb,sprintf('%s%i%s%i',"Loading DICOM images ",n,"/",L));
        handles.dicomSet(n).data = dicomread(sprintf('%s%s', ...
            handles.dicomdir, char(handles.dicomlist(int32(n)))));
    end
    
    handles.myinfo = handles.dicomSet(1); % To be removed (JSM 25102018)
%     % 'handles.myinfo' will keep the metadata of the dicom files loaded
%     handles.myinfo(1) = dicominfo(sprintf('%s%s', handles.dicomdir, ...
%         char(handles.dicomlist(1))),'UseDictionaryVR',true);

    % Temporal storing of metadata
    tempInfo=handles.dicomSet(1);
    save('tempInfo.mat','tempInfo');

    % Shows few metadata in the interface:
    %  - IPP identification number and Patient Initials
    set(handles.IPP_text, 'String', handles.dicomSet(1).PatientID)
    set(handles.initials_text,'String',sprintf('(%s%s)',...
        handles.dicomSet(1).PatientName.FamilyName(1),...
        handles.dicomSet(1).PatientName.GivenName(1)));
    set(handles.birthdate_text,'String',handles.dicomSet(1).PatientBirthDate);
    set(handles.gender_text,'String',handles.dicomSet(1).PatientSex);
    %  - CT resolution in mm
    set(handles.Resolution_text, 'String', sprintf('%f mm', handles.dicomSet(1).PixelSpacing(1)));
    %  - CT date
    set(handles.CTdate_text, 'String', sprintf('%s', handles.dicomSet(1).AcquisitionDate));
        
    % The following function sort the dicomFiles by their slice location
%     handles.dicomSetSorted=sortStructByField(handles.dicomSet,{'SliceLocation'});
    handles.dicomSetSorted=sortStructByField(handles.dicomSet,{'InstanceNumber'},handles);
    handles.dicomSetOld=handles.dicomSet;
    handles.dicomSet=handles.dicomSetSorted;
    'load finished'

catch except
    except
    except.identifier
    if strcmp(except.identifier,'Error identifier: MATLAB:nonExistentField')
        errordlg(except.message,'Loading Error')
%         return
%     elseif or(strcmp(except.identifier,'MATLAB:heterogeneousStrucAssignment'),...
%             strcmp(except.identifier,'MATLAB:heterogeneousStrucAssignment'))
%         f = errordlg(sprintf('%s\n\n%s\n%s', '   CT SCAN WITH UNEXPECTED ORIENTATION.',...
%             'Suggestion: mark the current folder as "Wrong_Orientation"',...
%             'and try with another set of CTs'),'Loading Error');
%         return
    else
        errordlg(sprintf('%s%s','Error identifier: ',except.identifier))
    end
end

%% Updating the radioButtons "NONE", "BONE"('BONE'), "SOFT"('STANDARD')
if isfield(handles.dicomSet(1), 'ConvolutionKernel')
    if strfind(handles.dicomSet(1).ConvolutionKernel, 'BONE')
        set(handles.radiobutton_none, 'Value', 0);
        set(handles.radiobutton_sharp, 'Value', 1);
        set(handles.radiobutton_smooth, 'Value', 0);
    elseif strfind(handles.dicomSet(1).ConvolutionKernel, 'STANDARD')
        set(handles.radiobutton_none, 'Value', 0);
        set(handles.radiobutton_sharp, 'Value', 0);
        set(handles.radiobutton_smooth, 'Value', 1);
    else
        set(handles.radiobutton_none, 'Value', 1);
        set(handles.radiobutton_sharp, 'Value', 0);
        set(handles.radiobutton_smooth, 'Value', 0);
    end
else
    set(handles.radiobutton_none, 'Value', 1);
    set(handles.radiobutton_sharp, 'Value', 0);
    set(handles.radiobutton_smooth, 'Value', 0);
end

%% Extracting data for interface representation
handles.slice = int32(handles.N / 2); % Chooses the central slice
% handles.mydicom(:,:,handles.slice) = dicomread(sprintf('%s%s', handles.dicomdir, char(handles.dicomlist(handles.slice))));
if isfield(handles,'mydicom')
    handles=rmfield(handles,'mydicom');
end
handles.mydicom(:,:,handles.slice) = handles.dicomSet(handles.slice).data;

handles.CTmin = -200;
handles.CTmax = 2000;

handles.bigmax = 3000;
handles.bigmin = -2000;

set(handles.slider_2Dcontrast, 'Max', handles.bigmax - handles.bigmin - 1);
set(handles.slider_2Dcontrast, 'Min', 0);
set(handles.slider_2Dcontrast, 'Value', 900);

set(handles.slider_2Dbrightness, 'Max', handles.bigmax);
set(handles.slider_2Dbrightness, 'Min', handles.bigmin);
set(handles.slider_2Dbrightness, 'Value', 1100);

set(handles.slice_num, 'String', handles.slice);

axes(handles.axes_2Dviewer); % Set current axes
% imshow(handles.mydicom(:,:,handles.slice), [handles.CTmin handles.CTmax]);
% imshow(handles.dicomSet(handles.slice).data, [handles.CTmin handles.CTmax]);
% trying dicomreadVolume
% [V, SPATIAL, DIM] = dicomreadVolume(handles.dicomdir);
% imshow(V(:,:,1,handles.slice), [handles.CTmin handles.CTmax]);
imshow(handles.dicomSet(handles.slice).data, [handles.CTmin handles.CTmax]);

%% ISOSURFACE section ====================================================
act3Dview_Callback(handles.act3Dview, eventdata, handles);

axes(handles.axes_2Dviewer); % Set current axes
guidata(hObject,handles);
% handles
if and(get(handles.patient_num,'String') ~="P###",...
        exist([char(get(handles.output_dir,'String')) '/readme'])==2)
    handles.text_readme.String="listo para leer";
end
% update_infoFields(handles);
% Makes handles variable visible to other functions in this script

%% Reset the DB chech result info box
set(handles.text_coincidences_info,'String',"Check DB for coincidences...");
guidata(hObject,handles); 


function act3Dview_Callback(hObject, eventdata, handles)
%% --- Executes on button press in act3Dview.
% hObject    handle to act3Dview (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of act3Dview
% handles.enable_3Dview = get(hObject,'Value')
if get(hObject,'Value')
    C=questdlg(['The 3D viewer might create memory problems when the CT'...
        ' contains more than 300 slices. Do you want to activate it?'],...
        '3D viewer activation','Yes, Display 3D view','Abort','Abort')
    switch C
        case 'Yes, Display 3D view' 
            handles.enable_3Dview = 1
        otherwise
            handles.enable_3Dview = 0
            set(hObject,'Value',0)
    end
else
    handles.enable_3Dview = 0
end
% clear handles.data 
axes(handles.isosurface); % Set current axes
cla

if isfield(handles,'N') & handles.enable_3Dview
    if handles.N>1
        directory=handles.dicomdir;
        % Preparing list of dicom full names (including address)
        for k=1:handles.N
            dicomListFullName(k)="";
            dicomListFullName(k)=[directory char(handles.dicomlist(k))];
        end
        try
            [V,spatial,dim] = dicomreadVolume(dicomListFullName);
            v = squeeze(V);
            v = double(v);
            v2= imresize3(v,0.2);
            handles.v2 = v2;
            handles.isoValue = 1400; % default limit for isosurface rendering
            p = patch(isosurface(v2,handles.isoValue));
            Sv2 = size(v2); 
            M = max(max(max(v2)));
            m = min(min(min(v2)));

            handles.bigmax = M; 
            handles.bigmin = m;
            set(handles.slider_3Dviewer, 'Max', handles.bigmax);
            set(handles.slider_3Dviewer, 'Min', handles.bigmin);
            set(handles.slider_3Dviewer, 'Value', handles.isoValue);

            d1=(M-m)/Sv2(1);
            d2=(M-m)/Sv2(2);
            d3=(M-m)/Sv2(3);
            [x,y,z]=meshgrid(m:d1:M,m:d2:M,m:d3:M);
            handles.x=x(1:Sv2(1),1:Sv2(2),1:Sv2(3));
            handles.y=y(1:Sv2(1),1:Sv2(2),1:Sv2(3));
            handles.z=z(1:Sv2(1),1:Sv2(2),1:Sv2(3));
            isocolors(handles.x,handles.y,handles.z,v2,p);
            p.FaceColor='interp';
            p.EdgeColor='none';
            view(-20, 10);
            % isosurface(v2,1400);
            rotate3d on;
        catch except
            if strcmp(except.identifier,'images:dicomread:differentPatientOrientations')
                f = errordlg(sprintf('%s\n\n%s\n%s', '   CT SCAN WITH UNEXPECTED ORIENTATION.',...
                    'Suggestion: mark the current folder as "Wrong_Orientation"',...
                    'and try with another set of CTs'),'Loading Error');
                % We change the folder name to mark it as scoutScan (if not marked before)
                if ~contains(handles.dicomdir,'wrong')
                    movefile([handles.dicomdir(1:end-1)],...
                        [handles.dicomdir(1:end-1) '_wrongOrientatedScan']);
                end
                return
            else
                errordlg(sprintf('%s%s','Error identifier: ',except.identifier));
                %         rethrow(except);
            end
        end
    end
end
guidata(hObject,handles); 


function slider_3Dviewer_Callback(hObject, eventdata, handles)
%% --- Executes on slider movement.
% hObject    handle to slider_3Dviewer (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
guidata(hObject,handles); 


function radiobutton_left_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_left.
% hObject    handle to radiobutton_left (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_left
handles.shoulder_side = 'Left';
update_readme_Callback(handles.update_readme,eventdata,handles);
guidata(hObject,handles); 

function radiobutton_right_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_right.
% hObject    handle to radiobutton_right (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_right
handles.shoulder_side = 'Right';
update_readme_Callback(handles.update_readme,eventdata,handles);
guidata(hObject,handles); 


%% --- Executes on button press in radiobutton_preop.
function radiobutton_preop_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton_preop (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_preop
handles.acquisition_stage = 'Preop';
update_readme_Callback(handles.update_readme,eventdata,handles);
% update_infoFields(handles);
guidata(hObject,handles); 

function radiobutton_postop_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_postop.
% hObject    handle to radiobutton_postop (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_postop
handles.acquisition_stage = 'Postop';
update_readme_Callback(handles.update_readme,eventdata,handles);
% update_infoFields(handles);
guidata(hObject,handles); 


function Check_Database_Callback(hObject, eventdata, handles)
%% --- Executes on button press in Check_Database.
% hObject    handle to Check_Database (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
wb = waitbar(0,'Checking Excel Database');
"Openning Excel Database"
% Checking Database -----------------------------------
% Importing database from excel file depending on computer system
% if computer('arch')=="win64"
%     handles.data=importDataBaseTab('../../../../data/Excel/ShoulderDataBase.xlsx','sCase',2,2000);
%     excelDB = '../../../../data/Excel/ShoulderDataBase.xlsx';
% else
% %     path2DB=[ '/home/shoulder/data/Excel/ShoulderDataBase.xlsx'];
%     system('ls /home/shoulder/data/Excel/');
%     path2DB=['/home/shoulder/data/Excel/ShoulderDataBase.xlsx'];
%     excelDB = '/home/shoulder/data/Excel/ShoulderDataBase.xlsx';
% %     ls('/home/shoulder/data/Excel/')
% %     f=importDataBaseTab_script;
%     handles.data=importDataBaseTab(path2DB,'sCase',2,2000);
%     
% end
% New way of reading the Excel Database:
[excelDB, DBpath, ~] = uigetfile('*.xlsx','Select the Excel Database File');
tic
E = exist(sprintf('%s%s',DBpath,excelDB));
% We store the Excel file adress and name for further use
handles.ExcelDB_path = DBpath;
handles.ExcelDB_fullname = sprintf('%s%s',DBpath,excelDB);

if E == 2 % Only if the file exist as a known format (XLS)
    [~,txt,raw,dates]=xlsread(handles.ExcelDB_fullname,'sCase','','',@convertSpreadsheetExcelDates);
    % The dates cell array will have NaN in every cell not containing a "date"
    dates(~cellfun(@(x) isnumeric(x) || islogical(x), dates)) = {NaN};
    handles.data.headers = string(txt(1,:));
    % Conversion of dates's cell array to numeric matrix
    dates=cell2mat(dates);
    % Finding columns with dates
    dates_CperR=find(~isnan(dates(1,:)));
    date_Cells{1}= dates_CperR;
    txt_Cells{1} = [];
    for p=2:size(txt,1)
        dates_CperR=find(~isnan(dates(p,:)));
        date_Cells{p}= dates_CperR;
        txt_CperR = find(~ismissing(txt(p,:)));
        txt_Cells{p} = txt_CperR;
    end
    date_columns = [];
    txt_columns = [];
    for p=1:length(date_Cells)
        date_columns= union(date_columns,date_Cells{p});
        txt_columns = union(txt_columns,txt_Cells{p});
    end
    num_columns = setdiff(1:size(raw,2),txt_columns);
    txt_columns = setdiff(txt_columns,date_columns);
    % Inverting the "date to number" convertion done during the importation
    dates_only = datetime(dates(2:end,[date_columns]),'ConvertFrom','Excel','Format','dd-MM-yyy');
%     num_only = cell2mat(raw(2:end,num_columns));
    
    for n=1:size(txt,2) % for each text headers (column)
        [data.(raw{1,n})]=raw(2:end,n);
    end
    k=1;
    for n=date_columns' % for the date columns
        [data.(raw{1,n})]=dates_only(:,k);
        k=k+1;
    end
    
elseif E == 0
    warndlg("Excel file not found!")
else
    warndlg("Database file has unrecognized format. It should be an Excel file")
end
toc
handles.data=data;

% ***Obtain the first row available for a new case***
% Get the colum of sCase.id, including those from rows available
sCase_list = handles.data.SCase_ID; 
% Cut the list from the end untill found an existing sCases
[s1,s2]=size(sCase_list);
s0=0;
while sCase_list(end,:)=="" % Last position empty...
    sCase_list = sCase_list(1:end-1,:);
    s0=s0+1;
    waitbar(s0/s1,wb,'Checking Excel Database');
end


sCase_N=[];
sCase_P=[];
% sCase_list_sorted=sort(sCase_list); % This helps to avoid errors if a row is eventually void
sCase_list_sorted=string(sCase_list); % This have to be cleaned
for n=1:s1-s0
    if sCase_list_sorted(n,:)~=""   
        L = length(char(extractAfter(sCase_list_sorted(n,:),1)));
        while L<3
            sCase_list_sorted(n,:)=sprintf('%s%s%s',...
                extractBefore(sCase_list_sorted(n,:),2),...
                '0',extractAfter(sCase_list_sorted(n,:),1));
            L = length(char(extractAfter(sCase_list_sorted(n,:),1)));
        end
        if extractBefore(sCase_list_sorted(n,:),2)=="N"
            sCase_N=[sCase_N; sCase_list_sorted(n,:)];
        elseif extractBefore(sCase_list_sorted(n,:),2)=="P"
            sCase_P=[sCase_P; sCase_list_sorted(n,:)];
        else
            "there is a row without identification (N or P) in the DataBase"
        end
        waitbar(s1-s0+n/s1,wb,'Checking Excel Database');
    end
end
sCase_N=sort(sCase_N);
sCase_P=sort(sCase_P);

% Build the next sCase.id for a potential new sCase
    % by extracting the 'id' number of the last sCase and adding '1' 
if handles.patient_group=="N"
    new_sCase = str2num(extractAfter(char(sCase_N(end)),1))+1; 
    % Finaly convert to string and add a 'P' for 'Pathological' 
    new_sCase = string(['N' num2str(new_sCase)]);
elseif handles.patient_group=="P"
    new_sCase = str2num(extractAfter(char(sCase_P(end)),1))+1; 
    % Finaly convert to string and add a 'N' for 'Normal' 
    new_sCase = string(['P' num2str(new_sCase)]);
end       
handles.data.anonymity_IPP=cell2mat(handles.data.anonymity_IPP);
handles.data.shoulder_side=cell2mat(handles.data.shoulder_side);

% *** Q1: Does the new IPP exist in the Database yet? ***
% Extract the list of patient IDs from Excel database
IPP_list_DB = handles.data.anonymity_IPP; 
% Extracting patient ID from dicom-set info
IPP_sCase = str2num(handles.myinfo(1).PatientID) 

% If the IPP of the current case already exist in the database, 
% it finds the position of the current patient ID in the list.
% And for this position it extracts the case name "sCase", otherwise it
% leave the variables empty
% handles.patientIndex=find(handles.data.anonymityIPP==str2num(handles.myinfo(1).PatientID))
handles.patientIndex=find(IPP_list_DB==IPP_sCase);
handles.sCase = handles.data.SCase_ID(handles.patientIndex);

% Determine how many sCases exits with the same IPP as the current CT
Ncoincidences=length(handles.sCase);

% *** We start the decision tree ***
if Ncoincidences==0
    % This is a new sCase!! So we write a short message and set the sCase
    set(handles.dataCheck_text,'String', sprintf('This is a new case'));
    set(handles.dataCheck_panel,'BackgroundColor','g');
    handles.current_sCase=new_sCase;
    set(handles.patient_num,'String',sprintf('%s',handles.current_sCase));
    set(handles.text_coincidences_info,'String',"Current IPP not found in DB");

% If the IPP exists in the Excel Database in more than one sCase we first
% can discriminate by the shoulder side (rigth or left)
elseif Ncoincidences>1
    % Launch a warning message
    set(handles.dataCheck_text,'String',...
        ['Patient found in ' num2str(Ncoincidences) ' sCase(s)']);
    set(handles.dataCheck_panel,'BackgroundColor','y');
    
    % Shows information of the 2 first coincidences
    coincidences = sprintf("%s \t%s \t%s \t%s \n%s \t%s \t%s \t\t%s \n%s \t%s \t%s \t\t%s",...
        "SCase","   IPP   ","   CT_date   ","Side",...
        string(handles.sCase(1)),...
        string(IPP_list_DB(handles.patientIndex(1))),...
        handles.data.CT_date(handles.patientIndex(1)),...
        handles.data.shoulder_side(handles.patientIndex(1)),...
        string(handles.sCase(2)),...
        string(IPP_list_DB(handles.patientIndex(2))),...
        handles.data.CT_date(handles.patientIndex(2)),...
        handles.data.shoulder_side(handles.patientIndex(2)));
    set(handles.text_coincidences_info,'String',coincidences);
        
    % *** Q2: is the current CT from the same side of one of the existing?
    % Get the side of the coincident sCases
    side_sCase = handles.data.shoulder_side(handles.patientIndex);
    % Launch 'question dialog' to let the user choose if one the coincident
    % sCases matches with the side (rigth or left) of the current CT
    question = sprintf("%s %s %s \n%s\n%s",...
        "The SCase",string(IPP_sCase),...
        "was found in the more than one case in the database.",...
        "Please, check the shoulder side of the currently loaded CT",...
        "and choose between the following options");
    title = "SCase found in database";
    btn1 = ['Existing case:' char(handles.sCase(1)) ' side:' char(side_sCase(1))];
    btn2 = ['Existing case:' char(handles.sCase(2)) ' side:' char(side_sCase(2))];
    btn3 = ['New case:' char(new_sCase) ' side: ?'];
    dfltbtn = btn3;
    answer = questdlg(question,title,btn1,btn2,btn3,dfltbtn);
    switch answer
        case btn1
            handles.current_sCase=handles.sCase(1);
            answerN = 1;
        case btn2
            handles.current_sCase=handles.sCase(2);
            answerN = 2;
        case btn3
            handles.current_sCase=string(new_sCase);
            answerN = 3;
        otherwise
            disp("Auto Check DB -ABORTED-");
            return;
    end
    disp(sprintf("%s %s",string(handles.current_sCase),"chosen"));
    
    % Update the list of sCases after selection
    handles.sCase=handles.current_sCase;
    Ncoincidences=1;
    
    % *** Q3: is the current CT date similar to the CT_date from any of the
    % concident sCases in the Database? ***
    
    % Get the CT's date from the coincident sCase from the Database
    try
        CTdate_DB = datestr(handles.data.CT_date(handles.patientIndex),'dd-mmm-yyyy');
    catch error
        message = sprintf("%s\n%s\n%s\n\n%s\n%s\n%s",...
            "Suggested solution:",...
            "Opt1. Update InfoCT.xlsx and repeat the 'Auto Check DB'",...
            "Opt2. Check the CT_date yourself and use 'Manual sCase'",...
            "Error details:",...
            error.identifier,error.message);
        errordlg(message,"Not valid CT_date found in Database");
        CTdate_DB = NaT;
    end
    % Get the CT's date from the new CT set
    current_CTdate = handles.myinfo.AcquisitionDate
    % Adapt date format to make it comparable
    current_CTdate=datestr([current_CTdate(1:4),'-',...
        current_CTdate(5:6),'-',current_CTdate(7:8)],'dd-mmm-yyyy')
    % Compare CT's dates
    if isequal(current_CTdate,CTdate_DB)
        % The sCase already exits so the user will have to decide if the CT
        % must be added to the case of it is already added.
        set(handles.dataCheck_text,'String',...
            ['Current CT matches in IPP, side and CTdate with others in the database']);
        set(handles.dataCheck_panel,'BackgroundColor','r');
        set(handles.patient_num,'String',string(handles.current_sCase));
    else
        % The user must check if the current CT set corresponds to a
        % post-op shoulder
        set(handles.dataCheck_text,'String',...
            ['Check if the CT is from a post-op. Current CT matches in IPP, side']);
        set(handles.dataCheck_panel,'BackgroundColor','r');
        set(handles.patient_num,'String',string(handles.current_sCase));
    end
        
% If only one sCase was found in the Database    
elseif Ncoincidences==1 
    % Launch a warning message
    set(handles.dataCheck_text,'String',...
        ['Patient found in one sCase(s)']);
    set(handles.dataCheck_panel,'BackgroundColor','r');
    handles.current_sCase=handles.sCase;
    
    coincidences = sprintf("%s \t%s \t%s \t%s \n%s \t%s \t%s \t\t%s",...
        "SCase","   IPP   ","   CT_date   ","Side",...
        string(handles.sCase(1)),...
        string(IPP_list_DB(handles.patientIndex(1))),...
        handles.data.CT_date(handles.patientIndex(1)),...
        handles.data.shoulder_side(handles.patientIndex(1)));
    set(handles.text_coincidences_info,'String',coincidences);
    
    side_sCase=handles.data.shoulder_side(handles.patientIndex);
    % Creating question dialog to let the user choose between the found
    % SCase and a new SCase label
    question = sprintf("%s %s %s \n%s\n%s",...
        "The loaded SCase",string(IPP_sCase),...
        "was found in the SCase list in the database.",...
        "Please, check the shoulder side of the currently loaded CT",...
        "and choose between the following options");
    title = "SCase found in database";
    btn1 = ['Existing case:' char(handles.sCase(1)) ' side:' char(side_sCase(1))];
    btn2 = ['New case:' char(new_sCase) ' side: ?'];
    dfltbtn = btn2;
    answer= questdlg(question,title,btn1,btn2,dfltbtn);
    
    switch answer
        case btn1
            handles.current_sCase=handles.sCase(1)
            answerN=1;
        case btn2
            handles.current_sCase=string(new_sCase);
            answerN=2;
        otherwise
            disp("Auto Check DB -ABORTED-");
            return;
    end
    disp(sprintf("%s %s",string(handles.current_sCase),"chosen"));
    
    if answerN==1
        
        % *** Q3: is the current CT date similar to the CT_date from any of the
        % concident sCases in the Database? ***
    
        % Get the CT's date from the coincident sCase from the Database
        try
            CTdate_DB = datestr(handles.data.CT_date(handles.patientIndex),'dd-mmm-yyyy');
        catch error
            message = sprintf("%s\n%s\n%s\n\n%s\n%s\n%s",...
                "Suggested solution:",...
                "Opt1. Update InfoCT.xlsx and repeat the 'Auto Check DB'",...
                "Opt2. Check the CT_date yourself and use 'Manual sCase'",...
                "Error details:",...
                error.identifier,error.message);
            errordlg(message,"Not valid CT_date found in Database");
            CTdate_DB = NaT;
        end
        % Get the CT's date from the new CT set
        current_CTdate = handles.myinfo.AcquisitionDate
        % Adapt date format to make it comparable
        current_CTdate=datestr([current_CTdate(1:4),'-',...
            current_CTdate(5:6),'-',current_CTdate(7:8)],'dd-mmm-yyyy')
        % Compare CT's dates
        if isequal(current_CTdate,CTdate_DB)
            % The sCase already exits so the user will have to decide if the CT
            % must be added to the case of it is already added.
            set(handles.dataCheck_text,'String',...
                ['Current CT matches in IPP, side and CTdate with others in the database']);
            set(handles.dataCheck_panel,'BackgroundColor','r');
            set(handles.patient_num,'String',sprintf('%s',string(handles.current_sCase)));
        else
            % The user must check if the current CT set corresponds to a
            % post-op shoulder
            set(handles.dataCheck_text,'String',...
                ['Check if the CT is from a post-op. Current CT matches in IPP, side']);
            set(handles.dataCheck_panel,'BackgroundColor','r');
            set(handles.patient_num,'String',sprintf('%s',string(handles.current_sCase)));
        end
    else
        % This is a new sCase!! So we write a short message and set the sCase
        set(handles.dataCheck_text,'String', sprintf('This is a new case'));
        set(handles.dataCheck_panel,'BackgroundColor','g');
        handles.current_sCase=new_sCase;
        set(handles.patient_num,'String',sprintf('%s',string(handles.current_sCase)));
    end 
end

F1=extractBefore(char(handles.current_sCase),2);
F2=extractBetween(char(handles.current_sCase),2,2);
F3=extractBetween(char(handles.current_sCase),3,3);

current_dir = cd(char(strcat(handles.base_dir,'/',F1,'/',F2,'/',F3))); % saving current directory and changing to the output dir
output_dir = pwd; % needed to update the output directory
cd(current_dir); % back to the current directory
set(handles.output_dir,'String',output_dir);
% set(handles.output_dir,'String',strcat(handles.base_dir,F1,'/',F2,'/',F3));%sprintf('%s%s\%s\%s',base_dir,F1,F2,F3));
waitbar(1,wb,'Checking Excel Database');
guidata(hObject,handles); 


function manual_case_selection_Callback(hObject, eventdata, handles)
%% --- Executes on button press in manual_case_selection.
% hObject    handle to manual_case_selection (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
sCase_dir = uigetdir(handles.base_dir);
set(handles.output_dir,'String',sCase_dir);
update_readme_Callback(handles.update_readme,eventdata,handles);
warndlg('Please uptade the sCase.id accordingly with the chosen output directory')
guidata(hObject,handles); 


function patient_num_Callback(hObject, eventdata, handles)
%% Executes with 'Enter' in patient_num
% hObject    handle to patient_num (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of patient_num as text
%        str2double(get(hObject,'String')) returns contents of patient_num as a double

% The output directory is stablish by the automatic Check of the DB or the
% manual selection. Hence, here we only check whether the sCase number
% matches with the selected output directory
% From "patient_num" which corresponds to sCase number
patient_num = get(handles.patient_num,'String'); % Get the sCase number
F0=char(extractBefore(char(patient_num),1)) 
F0=char(extractBefore(char(patient_num),2)) % Extract the 'N' or 'P'
F1=char(extractBetween(char(patient_num),2,2)) % Extract the first digit (1 to 9)
F2=char(extractBetween(char(patient_num),3,3)) % Extract the second digit (0to9)
% From "output_dir" which corresponds to output directory
output_dir = get(handles.output_dir,'String'); % Get the ourput directory
L = length(output_dir); % lenght of the string that contains the directory
D0=char(extractBetween(char(output_dir),L-4,L-4)) % Extact the 'N' or 'P'
D1=char(extractBetween(char(output_dir),L-2,L-2)) % Extract the first digit (1 to 9)
D2=char(extractAfter(char(output_dir),L-1)) % Extract the second digit (0 to 9)

if F0==D0 & F1==D1 & F2==D2
    handles.enable_importation = 1
else
    handles.enable_importation = 0
    warndlg('Importation cancelled. The sCase (patient number) must be consistant with the Output Directory')
end

guidata(hObject,handles); 



%% --- Executes on slider movement.
function slider_2Dslice_Callback(hObject, eventdata, handles)
% hObject    handle to slider_2Dslice (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
handles.slice = int32(get(hObject,'Value'));
set(handles.slice_num, 'String', handles.slice);
handles.mydicom(:,:,handles.slice) = handles.dicomSet(handles.slice).data;
axes(handles.axes_2Dviewer) % Set current axes
imshow(handles.mydicom(:,:,handles.slice), [handles.CTmin handles.CTmax])
guidata(hObject,handles);


function Import2database_Callback(hObject, eventdata, handles)
%% --- Executes on button press in Import2database.
% hObject    handle to Import2database (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

sortPictures = 1;

set(handles.info_text, 'String', 'Preparing DICOM images to be imported...');
drawnow
    
% Warning message in info panel when any patient number is found
if isempty(get(handles.patient_num,'String'))
    set(handles.info_text, 'ForegroundColor', 'red', 'FontWeight', 'bold', 'String', 'Please give a patient number')
    return
else
    patient = get(handles.patient_num,'String');
end

% W
if isempty(get(handles.output_dir,'String'))
    outputdir = uigetdir;
    if outputdir
        set(handles.output_dir,'String', outputdir);
    end
else
    outputdir = get(handles.output_dir,'String');
%     outputdir = outputdir{1};
end

if ~outputdir
    set(handles.info_text, 'ForegroundColor', 'red', 'FontWeight', 'bold',...
        'String', 'Please select an output directoy');
    return
end

set(handles.info_text, 'ForegroundColor', 'black', 'FontWeight', 'normal');

% Create name string
newname = [patient, '-', handles.dicomSet(1).PatientID, '_',...
    handles.dicomSet(1).PatientName.FamilyName(1),...
    handles.dicomSet(1).PatientName.GivenName(1)];
if get(handles.radiobutton_sharp,'Value')
    newname = [newname, '-bone.'];
elseif get(handles.radiobutton_smooth,'Value')
    newname = [newname, '-soft.'];
else
    newname = [newname, '.'];
end

% Create output directory
% outputdir = sprintf('%s%s%s%s%s%s%s%s%s%s%s',outputdir,'/', patient,'-',...
%     handles.dicomSet(1).PatientID,'/','CT-',patient,'-',...
%     handles.dicomSet(1).PatientID,handles.CTlabel_text.String,'/dicom/');
suggested_outputdir = sprintf('%s%s%s%s%s%s%s%s%s%s%s',outputdir,'/', patient,'-',...
    handles.dicomSet(1).PatientID,'/','CT-',patient,'-',...
    handles.dicomSet(1).PatientID,handles.CTlabel_text.String,'/dicom/');
if exist(suggested_outputdir)==7
    outputdir = sprintf('%s%s%s%s%s%s%s%s%s%s%s',outputdir,'/', patient,'-',...
        handles.dicomSet(1).PatientID,'/','CT-',patient,'-',...
        handles.dicomSet(1).PatientID,'xxx','/dicom/');
else
    outputdir = suggested_outputdir;
end
mkdir(outputdir);


% Sort pictures in correct order
if sortPictures == 1
    for h = 1:handles.N
        infoTemp = dicominfo(sprintf('%s%s', handles.dicomdir,...
            char(handles.dicomlist(h))),'UseDictionaryVR',true);
        SliceLoc(h,1) = h;
%         sprintf('%s%s', handles.dicomdir, char(handles.dicomlist(h)));
        SliceLoc(h,2) = infoTemp.SliceLocation;
    end
    SliceSorted = sortrows(SliceLoc,2);
end
guidata(hObject,handles); 

% Read all data
% at the importation we set the dicomSet as definitively sorted
handles.dicomSet=handles.dicomSetSorted; % with this sentence we could avoid the very previous sorting...
for i = 1:handles.N
    str = sprintf('Copying dicom...\n%d / %d\n', i, handles.N);
    set(handles.info_text, 'String', str);
    drawnow
    
    % This replace the Given Name by the patient inicials and kernel info 
    if get(handles.radiobutton_sharp,'Value')
        handles.dicomSet(i).PatientName.GivenName = ...
            [handles.dicomSet(i).PatientName.FamilyName(1),...
            handles.dicomSet(i).PatientName.GivenName(1), '_bone'];
    elseif get(handles.radiobutton_smooth,'Value')
        handles.dicomSet(i).PatientName.GivenName = ...
            [handles.dicomSet(i).PatientName.FamilyName(1),...
            handles.dicomSet(i).PatientName.GivenName(1), '_soft'];
    else
        handles.dicomSet(i).PatientName.GivenName = ...
            [handles.dicomSet(i).PatientName.FamilyName(1),...
            handles.dicomSet(i).PatientName.GivenName(1)];
    end
    % This replace the Given Name by the IPP
    handles.dicomSet(i).PatientName.FamilyName = [patient, '_',...
        handles.dicomSet(1).PatientID];

    % Importation
    dicomwrite(handles.dicomSet(i).data,[outputdir, newname,...
        sprintf('%04d',i), '.dcm'], handles.dicomSet(i));
end
guidata(hObject,handles); 

% Create readme.txt file if it does not exist already
localDir = string(get(handles.output_dir,'String'));
localDir = sprintf('%s%s%s%s%s%s',localDir,'/', patient,'-', handles.dicomSet(1).PatientID,'/');
if ~exist(sprintf('%s%s',localDir,'readme.txt'), 'file')
    readme_file=fopen(sprintf('%s%s',localDir,'readme.txt'), 'wt');
    fprintf(readme_file,sprintf('%s%s%s %s %s\r\n',patient,'-',...
        handles.dicomSet(1).PatientID,handles.initials_text.String,...
        handles.shoulder_side));
    fprintf(readme_file,sprintf('\r\n%s',get(handles.text_readme,'String')));
    fclose(readme_file);
else
    readme_file=fopen(sprintf('%s%s',localDir,'readme.txt'), 'at'); % opening to append text
    fprintf(readme_file,sprintf('\r\n%s',get(handles.text_readme,'String')));
    fclose(readme_file);
end

set(handles.info_text, 'String', 'Copied');
guidata(hObject,handles); 


function output_dir_Callback(hObject, eventdata, handles)
%%
% hObject    handle to output_dir (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of output_dir as text
%        str2double(get(hObject,'String')) returns contents of output_dir as a double
guidata(hObject,handles); 



function CTlabel_text_Callback(hObject, eventdata, handles)
% hObject    handle to CTlabel_text (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of CTlabel_text as text
%        str2double(get(hObject,'String')) returns contents of CTlabel_text as a double
update_readme_Callback(handles.update_readme,eventdata,handles);
guidata(hObject,handles); 


function output_dir_CreateFcn(hObject, eventdata, handles)
%% --- Executes during object creation, after setting all properties.
% hObject    handle to output_dir (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'),...
        get(0,'defaultUicontrolBackgroundColor'));
    set(hObject,'BackgroundColor','white');
end
guidata(hObject,handles); 



%% --- Executes during object creation, after setting all properties.
function info_text_CreateFcn(hObject, eventdata, handles)
% hObject    handle to info_text (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
guidata(hObject,handles); 


%% --- Executes during object creation, after setting all properties.
function DicomInfoBox_CreateFcn(hObject, eventdata, handles)
% hObject    handle to info_text (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called
guidata(hObject,handles); 




%% --- Executes during object creation, after setting all properties.
function slider_3Dviewer_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_3Dviewer (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end
guidata(hObject,handles); 


%% --- Executes on button press in DicomDetails.
function DicomDetails_Callback(hObject, eventdata, handles)
% hObject    handle to DicomDetails (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
try
    load tempInfo.mat
    tempInfo
    handles.DicomInfoBox.String = ['Dicom Info: ',...
        'Patient Sex: ', handles.dicomSet(1).PatientSex,...
        '. Birthday: ', handles.dicomSet(1).PatientBirthDate];
catch exception
    "Dicom info not available"
end
guidata(hObject,handles); 


% function checkbox_IPP_Callback(hObject, eventdata, handles)
% %% --- Executes on button press in checkbox_IPP.
% % hObject    handle to checkbox_IPP (see GCBO)
% % eventdata  reserved - to be defined in a future version of MATLAB
% % handles    structure with handles and user data (see GUIDATA)
% 
% % Hint: get(hObject,'Value') returns toggle state of checkbox_IPP
% if get(hObject,'Value') %the IPP must be added to the readme line
%     try
%         handles.readme.IPP = string(handles.sCase);
%         ['IPP info to be added to the Readme line := ' handles.readme.IPP]
%     catch except
%         sprintf('%s%s','Error identifier: ',except.identifier)
%         ['IPP info failed to be added to the Readme line.']
%         handles.readme.IPP = '';
%     end
% else
%     handles.readme.IPP = '';
%     ['IPP info not present in Readme line']
% end
% % update_infoFields(handles);
% update_readme_Callback(handles.update_readme,eventdata,handles);
% guidata(hObject,handles); 
        

function checkbox_CTdate_Callback(hObject, eventdata, handles)
%% --- Executes on button press in checkbox_CTdate.
% hObject    handle to checkbox_CTdate (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of checkbox_CTdate
if get(hObject,'Value') %the IPP must be added to the readme line
    try
        handles.readme.CTdate = string(handles.myinfo(1).AcquisitionDate);
        ['CTdate info to be added to the Readme line := ' handles.readme.CTdate]
    catch except
        sprintf('%s%s','Error identifier: ',except.identifier)
        ['CTdate info failed to be added to the Readme line.']
        handles.readme.CTdate = '';
    end
else
    handles.readme.CTdate = '';
    ['CTdate info not present in Readme line']
end
% update_infoFields(handles);
update_readme_Callback(handles.update_readme,eventdata,handles);
guidata(hObject,handles); 
        

function checkbox_resolution_Callback(hObject, eventdata, handles)
%% --- Executes on button press in checkbox_resolution.
% hObject    handle to checkbox_resolution (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of checkbox_resolution
if get(hObject,'Value') %the IPP must be added to the readme line
    try
        handles.readme.resolution = string(handles.myinfo(1).PixelSpacing(1));
        ['Resolution info to be added to the Readme line := ' handles.readme.resolution]
    catch except
        sprintf('%s%s','Error identifier: ',except.identifier)
        ['Resolution info failed to be added to the Readme line.']
        handles.readme.resolution = '';
    end
else
    handles.readme.resolution = '';
    ['Resolution info not present in Readme line']
end
% update_readme_line(handles)
% update_infoFields(handles);
update_readme_Callback(handles.update_readme,eventdata,handles);
guidata(hObject,handles); 


function radiobutton_shoulder_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_shoulder.
% hObject    handle to radiobutton_shoulder (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_shoulder
handles.body = 'Shoulder';
set(handles.checkbox_contralateral,'Value',0);
handles.contralateral='';
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 

function radiobutton_elbow_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_elbow.
% hObject    handle to radiobutton_elbow (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_elbow
handles.body = 'Elbow';
set(handles.checkbox_contralateral,'Value',0);
handles.contralateral='';
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 


function radiobutton_thorax_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_thorax.
% hObject    handle to radiobutton_thorax (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_thorax
handles.body = 'Thorax';
set(handles.checkbox_contralateral,'Value',0);
handles.contralateral='';
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 


function checkbox_contralateral_Callback(hObject, eventdata, handles)
%% --- Executes on button press in checkbox_contralateral.
% hObject    handle to checkbox_contralateral (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of checkbox_contralateral
if get(handles.checkbox_contralateral,'Value')
    handles.contralateral = ['Contralateral '];
else
    handles.contralateral = '';
end
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 


function radiobutton_otherBody_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_otherBody.
% hObject    handle to radiobutton_otherBody (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_otherBody
set(handles.checkbox_contralateral,'Value',0);
handles.contralateral='';
set(handles.edit_otherBody,'Enable','On');
handles.body = get(handles.edit_otherBody,'String');
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 

function edit_otherBody_Callback(hObject, eventdata, handles)
%%
% hObject    handle to edit_otherBody (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit_otherBody as text
%        str2double(get(hObject,'String')) returns contents of edit_otherBody as a double
handles.body = get(handles.edit_otherBody,'String');
guidata(hObject,handles); 


function radiobutton_sharp_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_sharp.
% hObject    handle to radiobutton_sharp (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_sharp
% 
% if get(hObject,'Value')
%     set(handles.radiobutton_none,'Value',0);
%     set(handles.radiobutton_smooth,'Value',0);
% else
%     set(hObject,'Value',1);
% end
handles.kernel='Sharp';
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 

function radiobutton_smooth_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_smooth.
% hObject    handle to radiobutton_smooth (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_smooth
% 
% if get(hObject,'Value')
%     set(handles.radiobutton_none,'Value',0);
%     set(handles.radiobutton_sharp,'Value',0);
% else
%     set(hObject,'Value',1);
% end
handles.kernel='Smooth';
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 

function radiobutton_none_Callback(hObject, eventdata, handles)
%% --- Executes on button press in radiobutton_none.
% hObject    handle to radiobutton_none (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_none
handles.kernel='none';
warndlg(char("IMPORTANT: The operator must choose between 'Sharp (Bone)' or 'Smooth (Soft Tissue)'"));
update_readme_Callback(handles.update_readme,eventdata,handles);
guidata(hObject,handles); 


function checkbox_with_phantoms_Callback(hObject, eventdata, handles)
%% --- Executes on button press in checkbox_with_phantoms.
% hObject    handle to checkbox_with_phantoms (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of checkbox_with_phantoms
handles.phantoms = 'with';
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 


function radiobutton_without_phantoms_Callback(hObject, eventdata, handles)
% --- Executes on button press in radiobutton_without_phantoms.
% hObject    handle to radiobutton_without_phantoms (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton_without_phantoms
handles.phantoms = 'without';
update_readme_Callback(handles.update_readme, eventdata, handles);
guidata(hObject,handles); 


function edit_extra_Callback(hObject, eventdata, handles)
%% 
% hObject    handle to edit_extra (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit_extra as text
%        str2double(get(hObject,'String')) returns contents of edit_extra as a double
guidata(hObject,handles); 


function update_readme_Callback(hObject, eventdata, handles)
%% --- Executes on button press in update_readme.
% hObject    handle to update_readme (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if ~isfield(handles,'shoulder_side')
    handles.shoulder_side = '*Sh_Side*';
end
if ~isfield(handles,'acquisition_stage')
    handles.acquisition_stage = '*Pre-o-Post_op*';
end
% handles.patient_num always exists
% handles.IPP_text
% handles.CTdate_text
% handles.Resolution_text
% handles.CTlabel_text
if ~isfield(handles,'body')
    handles.body = '*body*';
end
if ~isfield(handles,'kernel')
    handles.kernel = '*kernel*';
end
if ~isfield(handles,'phantoms')
    handles.phantoms = '*phantoms*';
end
if ~isfield(handles,'contralateral')
    handles.contralateral = '';
end
if ~isfield(handles,'N')
    handles.N = 0;
end

% choosing handles.CTlabel_text
switch handles.acquisition_stage
    case 'Preop'
        if ~get(handles.checkbox_contralateral,'Value')
            switch handles.body
                case 'Shoulder'
                    switch handles.phantoms
                        case 'without'
                            switch handles.kernel
                                case 'Sharp'
                                    handles.CTlabel_text.String = '-1';
                                case 'Smooth'
                                    handles.CTlabel_text.String = '-2';
                                otherwise
                                    handles.CTlabel_text.String = '-xxx';
                                    warndlg('Operator must choose between Sharp or Smooth kernel');
                            end
                        case 'with'
                            switch handles.kernel
                                case 'Sharp'
                                    handles.CTlabel_text.String = '-3';
                                case 'Smooth'
                                    handles.CTlabel_text.String = '-4';
                                otherwise
                                    handles.CTlabel_text.String = '-xxx';
                                    warndlg('Operator must choose between Sharp or Smooth kernel');
                            end
                        otherwise
                            handles.CTlabel_text.String = '-xxx';
                    end
                case 'Elbow'
                    switch handles.kernel
                        case 'Sharp'
                            handles.CTlabel_text.String = '-5';
                        case 'Smooth'
                            handles.CTlabel_text.String = '-6';
                        otherwise
                            handles.CTlabel_text.String = '-xxx';
                            warndlg('Operator must choose between Sharp or Smooth kernel');
                    end
                case 'Thorax'
                    switch handles.kernel
                        case 'Sharp'
                            handles.CTlabel_text.String = '-7';
                        case 'Smooth'
                            handles.CTlabel_text.String = '-8';
                        otherwise
                            handles.CTlabel_text.String = '-xxx';
                            warndlg('Operator must choose between Sharp or Smooth kernel');
                    end
                otherwise
                    handles.CTlabel_text.String = '-x11';
            end
        else
            switch handles.kernel
                case 'Sharp'
                    handles.CTlabel_text.String = '-9';
                case 'Smooth'
                    handles.CTlabel_text.String = '-10';
                otherwise
                    handles.CTlabel_text.String = '-xxx';
                    warndlg('Operator must choose between Sharp or Smooth kernel');
            end
        end
    case 'Postop'
        if ~get(handles.checkbox_contralateral,'Value')
            switch handles.body
                case 'Shoulder'
                    switch handles.phantoms
                        case 'without'
                            switch handles.kernel
                                case 'Sharp'
                                    handles.CTlabel_text.String = '-p1';
                                case 'Smooth'
                                    handles.CTlabel_text.String = '-p2';
                                otherwise
                                    handles.CTlabel_text.String = '-pxxx';
                                    warndlg('Operator must choose between Sharp or Smooth kernel');
                            end
                        case 'with'
                            switch handles.kernel
                                case 'Sharp'
                                    handles.CTlabel_text.String = '-p3';
                                case 'Smooth'
                                    handles.CTlabel_text.String = '-p4';
                                otherwise
                                    handles.CTlabel_text.String = '-pxxx';
                                    warndlg('Operator must choose between Sharp or Smooth kernel');
                            end
                        otherwise
                            handles.CTlabel_text.String = '-pxxx';
                    end
                case 'Elbow'
                    switch handles.kernel
                        case 'Sharp'
                            handles.CTlabel_text.String = '-p5';
                        case 'Smooth'
                            handles.CTlabel_text.String = '-p6';
                        otherwise
                            handles.CTlabel_text.String = '-pxxx';
                            warndlg('Operator must choose between Sharp or Smooth kernel');
                    end
                case 'Thorax'
                    switch handles.kernel
                        case 'Sharp'
                            handles.CTlabel_text.String = '-p7';
                        case 'Smooth'
                            handles.CTlabel_text.String = '-p8';
                        otherwise
                            handles.CTlabel_text.String = '-pxxx';
                            warndlg('Operator must choose between Sharp or Smooth kernel');
                    end
                otherwise
                    handles.CTlabel_text.String = '-px11';
            end
        else
            switch handles.kernel
                case 'Sharp'
                    handles.CTlabel_text.String = '-p9';
                case 'Smooth'
                    handles.CTlabel_text.String = '-p10';
                otherwise
                    handles.CTlabel_text.String = '-pxxx';
                    warndlg('Operator must choose between Sharp or Smooth kernel');
            end
        end
    otherwise
        handles.CTlabel_text.String = '-xxx';
end

RL = sprintf('%s%s%s%s%s %s %s %s %s %s %s %s %s ','CT-',...
    handles.patient_num.String,'-',...
    handles.IPP_text.String,...
    handles.CTlabel_text.String,...
    handles.contralateral,...
    handles.body,...
    handles.kernel,...
    handles.phantoms,'phantoms',...
    handles.Resolution_text.String,...
    string(handles.N),'slices'),...
    get(handles.edit_extra,'String');
set(handles.text_readme,'String',RL);
guidata(hObject,handles); 


function add_newSCase_excelDB_Callback(hObject, eventdata, handles)
%% --- Executes on button press in add_newSCase_excelDB.
% hObject    handle to add_newSCase_excelDB (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Text info to the command window
sprintf('%s:\n%s, %s, %s, %s,\n%s, %s, %s,',"The parameters to write in the Excel Database are",...
    "SCase_ID","SCase_idx","anonymity_IPP","anonymity_initials",...
    "anonymity_bithDate","patient_gender","shoulder_side")

% The file SCaseImport.xlsx must be located inside the subfolder
% xlsFromMatlab/ which is in the same directory of the main Database Excel
ExcelImport_fullname = sprintf('%s%s',handles.ExcelDB_path,"xlsFromMatlab/SCaseImport.xlsx");
sprintf("%s%s", "Writting in file ", ExcelImport_fullname)

% In order to avoid the repetition of any SCase we have to read and check
% the SCaseImport.xlsx file:
[~,txt,raw,dates]=xlsread(ExcelImport_fullname,'SCaseImport','','',@convertSpreadsheetExcelDates);
% Looking for the "desired new SCase" in the existing list of SCases of
% SCaseImport.xlsx
% Removing void rows
raw=raw(find(string(raw(:,1))~=''),:);
found_SCase_Index = find(string(raw(:,1))==handles.patient_num.String);
new_SCase_Index = length(string(raw(:,1)))+1; 

% If there is no coincidence we set the desired SCase as a new one and can
% allow to write the new line of Import Parameters. Otherwise we will ask
% to overwrite the existing line of parameters or doing nothing.
if isempty(found_SCase_Index)
    SCase_Index = new_SCase_Index;
else
    question = "The chosen SCase already exist. Do you want to overwrite it?";
    title = "WARNING: SCase repeated";
    btn1 = "Cancel";
    btn2 = "Overwrite";
    dfltbtn = "Cancel";
    answer = questdlg(question,title,btn1,btn2,dfltbtn);
    % Handle response
    switch answer
        case "Overwrite"
            SCase_Index = found_SCase_Index;
        case "Cancel"
            disp("new SCase parameter line aborted")
            return;
        otherwise 
            disp("new SCase parameter line aborted")
            return;
    end
end
% I don't know why this writting is taking a wrong ROW
rowNumber=SCase_Index;
new_SCase_ID = {handles.patient_num.String};
% Wrtitting SCase_ID
SCaseCell=sprintf('%s%i','A',rowNumber);
 % Security Check: avoiding doubling SCases
if isempty(find(string(handles.data.SCase_ID)==string(new_SCase_ID)))
    "SCase_ID written"
    xlswrite(ExcelImport_fullname,new_SCase_ID,'SCaseImport',SCaseCell)
else
    "The selected SCase_ID is already present in the Database"
    return
end
% Wrtitting SCase_idx
IdxCell=sprintf('%s%i','B',rowNumber);
xlswrite(ExcelImport_fullname,rowNumber,'SCaseImport',IdxCell)
% Wrtitting anonymity_IPP
IPP_number = str2num(handles.IPP_text.String);
IPPCell=sprintf('%s%i','C',rowNumber);
xlswrite(ExcelImport_fullname,IPP_number,'SCaseImport',IPPCell)
% Wrtitting anonymity_initials
Initials={extractBefore(extractAfter(handles.initials_text.String,'('),')')};
InitialsCell=sprintf('%s%i','D',rowNumber);
xlswrite(ExcelImport_fullname,Initials,'SCaseImport',InitialsCell)
% Wrtitting anonymity_birthDate
BirthDate ={[handles.birthdate_text.String(1:4) ...
    '-' handles.birthdate_text.String(5:6) ...
    '-' handles.birthdate_text.String(7:8)]};
BirthDateCell=sprintf('%s%i','E',rowNumber);
xlswrite(ExcelImport_fullname,BirthDate,'SCaseImport',BirthDateCell)
% Wrtitting patient_gender
GenderCell=sprintf('%s%i','F',rowNumber);
Patient_Gender = handles.gender_text.String;
xlswrite(ExcelImport_fullname,Patient_Gender,'SCaseImport',GenderCell)
% Wrtitting shoulder_side
ShSideCell=sprintf('%s%i','G',rowNumber);
Shoulder_Side = handles.shoulder_side(1);
xlswrite(ExcelImport_fullname,Shoulder_Side,'SCaseImport',ShSideCell)

%launch 'dicominfoSCase.m' to update CTdicomInfo CSV and XLS
currentFolder=pwd;
cd([currentFolder '/..'])
dicominfoSCase % Lauched without arguments a avoid current error (1'20")
cd(currentFolder)
msgbox("Operation completed!. Remember to add manually SCase_ID and SCase_idx")


%% Internal functions

function update_readme_line(handles)
%% -- Updates readme line
% Complete the line to be writen in the readme file as:
% CT-P454-513554-1 sharp shoulder without phantoms 0.351562 mm 137 slices
try
    handles.readme.IPP = handle.myinfo.PatientID;
    handles.readme.CTdate = handles.myinfo.AcquisitionDate;
    handles.readme.CT_label = handles.CTlabel_text;
    if handles.radiobutton_sharp
        handles.readme.kernel = 'Sharp (BONE)';
    elseif handles.radiobutton_smooth
        handles.readme.kernel = 'Smooth (SOFT)';
    else
        handles.readme.kernel = 'None';
    end
    

    handles.readme.line = ['CT-' handles.readme.IPP '-' handles.readme.CT_label...
        ' ' handles.readme.kernel ' ' handles.readme.body ' '...
        handles.readme.phantoms ' ' handles.readme.resolution ' ' ...
        handles.readme.slices ' ' handles.readme.stage ' ' handles.readme.extra...
        ' ']
catch except
    sprintf('%s%s','Error identifier: ',except.identifier)
    'fields lacking'
    
end
guidata(hObject,handles); 

function sortedST = sortStructByField(ST,field,handles)
try
    "internal fuction activated"
    STfields = fieldnames(ST);
    STcell = struct2cell(ST);
    sz = size(STcell);      % Notice that this is a 3 dimensional array.
                            % For MxN structure array with P fields, the size
                            % of the converted cell array is PxMxN

    % Once it's a cell array, you can sort using sortrows:

    % Convert to a matrix
    STcell = reshape(STcell, sz(1), []);      % Px(MxN)

    % Make each field a column
    STcell = STcell';                         % (MxN)xP

    column=0
    % Sort by field 
    for k=1:length(STfields)
        if isequal(STfields(k),field)
            column = k;
        end
    end
    % fieldName=char(STfields(1))
    % field=char(field)
    % fieldColum = find(fieldName(1:length(field))==field)
    if column == 0
        ['Warning: field ' char(field) ' not found in dicom metadata']
        sortedST = ST;
        return
    else
        fieldColumn = column;
        STcell = sortrows(STcell, fieldColumn);

        %And convert it back to a structure array:

        % Put back into original cell array format
       STcell = reshape(STcell', sz);

       % Convert to Struct
       STsorted = cell2struct(STcell, STfields, 1);
       sortedST = STsorted;
    end
catch except
    except.identifier
    except.message
    ['exception arised during dicom sorting by field']
end



% function update_infoFields(hObject, handles)
% %% Updating CT labelling
% %     if and(get(handles.patient_num,'String') ~='P###',exist([handles.output_dir '/readme'])==2)
% %         set(handles.text_readme, "listo para leer")
% %     end
% guidata(hObject,handles); 


%% Functions to be removed

function slider_2Dcontrast_Callback(hObject, eventdata, handles)
%% --- Executes on slider movement.
% hObject    handle to slider_2Dcontrast (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

if ~isfield(handles, 'mydicom');
    return
end

handles.CTmax = (get(handles.slider_2Dbrightness,'Max') + get(handles.slider_2Dbrightness,'Min') - get(handles.slider_2Dbrightness,'Value')) + (get(hObject,'Max') - get(hObject,'Value'))/2;
handles.CTmin = (get(handles.slider_2Dbrightness,'Max') + get(handles.slider_2Dbrightness,'Min') - get(handles.slider_2Dbrightness,'Value')) - (get(hObject,'Max') - get(hObject,'Value'))/2;

if handles.CTmax > handles.bigmax
    handles.CTmax = handles.bigmax;
end

if handles.CTmin < handles.bigmin
    handles.CTmin = handles.bigmin;
end

imshow(handles.mydicom(:,:,handles.slice), [handles.CTmin handles.CTmax]);

guidata(hObject,handles)


function slider_2Dcontrast_CreateFcn(hObject, eventdata, handles)
%% --- Executes during object creation, after setting all properties.
% hObject    handle to slider_2Dcontrast (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end
guidata(hObject,handles); 


function slider_2Dbrightness_Callback(hObject, eventdata, handles)
%% --- Executes on slider movement.
% hObject    handle to slider_2Dbrightness (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider

if ~isfield(handles, 'mydicom');
    return
end

handles.CTmax = (get(hObject,'Max') + get(hObject,'Min')...
    - get(hObject,'Value')) + (get(handles.slider_2Dcontrast,'Max')...
    - get(handles.slider_2Dcontrast,'Value'))/2;
handles.CTmin = (get(hObject,'Max') + get(hObject,'Min')...
    - get(hObject,'Value')) - (get(handles.slider_2Dcontrast,'Max')...
    - get(handles.slider_2Dcontrast,'Value'))/2;

if handles.CTmax > handles.bigmax
    handles.CTmax = handles.bigmax;
end

if handles.CTmin < handles.bigmin
    handles.CTmin = handles.bigmin;
end

imshow(handles.mydicom(:,:,handles.slice), [handles.CTmin handles.CTmax]);

guidata(hObject,handles);


function slider_2Dbrightness_CreateFcn(hObject, eventdata, handles)
%% --- Executes during object creation, after setting all properties.
% hObject    handle to slider_2Dbrightness (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end
guidata(hObject,handles);